Communication between colvars and NAMD (implementation of colvarproxy) More...

#include <colvarproxy_namd.h>

Inheritance diagram for colvarproxy_namd:

Public Member Functions
void	init_tcl_pointers () override

	colvarproxy_namd ()

	~colvarproxy_namd ()

int	setup () override

int	reset () override

int	update_target_temperature ()
	Get the target temperature from the NAMD thermostats supported so far. More...

void	init_atoms_map ()
	Allocate an atoms map with the same size as the NAMD topology. More...

int	update_atoms_map (AtomIDList::const_iterator begin, AtomIDList::const_iterator end)

void	calculate ()

void	log (std::string const &message) override

void	error (std::string const &message) override

int	set_unit_system (std::string const &units_in, bool check_only) override

void	add_energy (cvm::real energy) override

void	request_total_force (bool yesno) override

bool	total_forces_enabled () const override

int	run_force_callback () override

int	run_colvar_callback (std::string const &name, std::vector< const colvarvalue *> const &cvcs, colvarvalue &value) override

int	run_colvar_gradient_callback (std::string const &name, std::vector< const colvarvalue *> const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient) override

cvm::real	rand_gaussian () override

cvm::real	get_accelMD_factor () const override

bool	accelMD_enabled () const override

int	check_replicas_enabled () override

int	replica_index () override

int	num_replicas () override

void	replica_comm_barrier () override

int	replica_comm_recv (char *msg_data, int buf_len, int src_rep) override

int	replica_comm_send (char *msg_data, int msg_len, int dest_rep) override

int	check_atom_name_selections_available () override

int	init_atom (int atom_number) override

int	check_atom_id (int atom_number) override

int	init_atom (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override

int	check_atom_id (cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override

void	clear_atom (int index) override

void	update_atom_properties (int index)

cvm::rvector	position_distance (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const

int	load_atoms_pdb (char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double const pdb_field_value) override

int	load_coords_pdb (char const *filename, std::vector< cvm::atom_pos > &pos, const std::vector< int > &indices, std::string const &pdb_field, double const pdb_field_value) override

int	scalable_group_coms () override

int	init_atom_group (std::vector< int > const &atoms_ids) override

void	clear_atom_group (int index) override

int	update_group_properties (int index)

int	check_volmaps_available () override

int	init_volmap_by_id (int volmap_id) override

int	init_volmap_by_name (const char *volmap_name) override

int	check_volmap_by_id (int volmap_id) override

int	check_volmap_by_name (char const *volmap_name) override

int	get_volmap_id_from_name (char const *volmap_name) override

void	clear_volmap (int index) override

int	compute_volmap (int flags, int volmap_id, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real value, cvm::real atom_field) override

template<class T >
void	getGridForceGridValue (int flags, T const grid, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real value, cvm::real *atom_field)
	Abstraction of the two types of NAMD volumetric maps. More...

template<class T , int flags>
void	GridForceGridLoop (T const g, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real value, cvm::real *atom_field)
	Implementation of inner loop; allows for atom list computation and use. More...

std::ostream &	output_stream (std::string const &output_name, std::string const description) override

int	flush_output_stream (std::string const &output_name) override

int	flush_output_streams () override

int	close_output_stream (std::string const &output_name) override

int	close_output_streams () override

int	backup_file (char const *filename) override

int	get_alch_lambda (cvm::real *lambda)
	Get value of alchemical lambda parameter from back-end. More...

int	send_alch_lambda (void)
	Set value of alchemical lambda parameter in back-end. More...

int	request_alch_energy_freq (int const freq)
	Request energy computation every freq steps. More...

int	get_dE_dlambda (cvm::real *dE_dlambda)
	Get energy derivative with respect to lambda. More...

Public Member Functions inherited from GlobalMaster
void	processData (AtomIDList::iterator a_i, AtomIDList::iterator a_e, PositionList::iterator p_i, PositionList::iterator g_i, PositionList::iterator g_e, BigRealList::iterator gm_i, BigRealList::iterator gm_e, ForceList::iterator gtf_i, ForceList::iterator gtf_e, IntList::iterator goi_i, IntList::iterator goi_e, BigRealList::iterator gov_i, BigRealList::iterator gov_e, AtomIDList::iterator last_atoms_forced_i, AtomIDList::iterator last_atoms_forced_e, ForceList::iterator last_forces_i, AtomIDList::iterator, AtomIDList::iterator, ForceList::iterator)

bool	changedAtoms ()

const AtomIDList &	requestedAtoms ()

bool	changedForces ()

const AtomIDList &	forcedAtoms ()

const ForceList &	appliedForces ()

bool	changedGroups ()

const ResizeArray< AtomIDList > &	requestedGroups ()

const ForceList &	groupForces ()

bool	changedGridObjs ()

const IntList &	requestedGridObjs ()

const BigRealList &	gridObjForces ()

bool	requestedTotalForces ()

void	clearChanged ()

virtual	~GlobalMaster ()

void	check () const

void	setLattice (const Lattice *lat)

Protected Member Functions
void	update_accelMD_info ()

Protected Member Functions inherited from GlobalMaster
	GlobalMaster ()

AtomIDList &	modifyRequestedAtoms ()

AtomIDList &	modifyForcedAtoms ()

ForceList &	modifyAppliedForces ()

ResizeArray< AtomIDList > &	modifyRequestedGroups ()

ForceList &	modifyGroupForces ()

IntList &	modifyRequestedGridObjects ()

BigRealList &	modifyGridObjForces ()

AtomIDList::const_iterator	getAtomIdBegin ()

AtomIDList::const_iterator	getAtomIdEnd ()

PositionList::const_iterator	getAtomPositionBegin ()

PositionList::const_iterator	getGroupPositionBegin ()

PositionList::const_iterator	getGroupPositionEnd ()

ForceList::const_iterator	getGroupTotalForceBegin ()

ForceList::const_iterator	getGroupTotalForceEnd ()

IntList::const_iterator	getGridObjIndexBegin ()

IntList::const_iterator	getGridObjIndexEnd ()

BigRealList::const_iterator	getGridObjValueBegin ()

BigRealList::const_iterator	getGridObjValueEnd ()

AtomIDList::const_iterator	getLastAtomsForcedBegin ()

AtomIDList::const_iterator	getLastAtomsForcedEnd ()

ForceList::const_iterator	getLastForcesBegin ()

AtomIDList::const_iterator	getForceIdBegin ()

AtomIDList::const_iterator	getForceIdEnd ()

ForceList::const_iterator	getTotalForce ()

void	requestTotalForce (bool yesno=true)

BigRealList::const_iterator	getGroupMassBegin ()

BigRealList::const_iterator	getGroupMassEnd ()

void	addReductionEnergy (int reductionTag, BigReal energy)

SubmitReduction *	getCurrentReduction ()

void	submitReduction ()

Protected Attributes
std::vector< int >	atoms_map
	Array of atom indices (relative to the colvarproxy arrays), usedfor faster copy of atomic data. More...

SimParameters *	simparams
	Pointer to the NAMD simulation input object. More...

Controller const *	controller
	Pointer to Controller object. More...

Random	random
	NAMD-style PRNG object. More...

bool	first_timestep

cvm::step_number	previous_NAMD_step

bool	accelMDOn
	Used to submit restraint energy as MISC. More...

cvm::real	amd_weight_factor

Protected Attributes inherited from GlobalMaster
bool	totalForceRequested

const Lattice *	lattice

AtomIDList::iterator	atomIdBegin

AtomIDList::iterator	atomIdEnd

PositionList::iterator	atomPositionBegin

PositionList::iterator	groupPositionBegin

PositionList::iterator	groupPositionEnd

BigRealList::iterator	groupMassBegin

BigRealList::iterator	groupMassEnd

ForceList::iterator	groupTotalForceBegin

ForceList::iterator	groupTotalForceEnd

IntList::iterator	gridObjIndexBegin

IntList::iterator	gridObjIndexEnd

BigRealList::iterator	gridObjValueBegin

BigRealList::iterator	gridObjValueEnd

AtomIDList::iterator	lastAtomsForcedBegin

ForceList::iterator	lastForcesBegin

AtomIDList::iterator	lastAtomsForcedEnd

AtomIDList::iterator	forceIdBegin

AtomIDList::iterator	forceIdEnd

ForceList::iterator	totalForceBegin

bool	reqAtomsChanged

AtomIDList	reqAtoms

bool	appForcesChanged

AtomIDList	fAtoms

ForceList	appForces

bool	reqGroupsChanged

ResizeArray< AtomIDList >	reqGroups

ForceList	grpForces

bool	reqGridObjsChanged

IntList	reqGridObjs

BigRealList	gridobjForces

Friends
class	cvm::atom

Additional Inherited Members
Public Attributes inherited from GlobalMaster
int	step

int	globalMasterStep

int	old_num_groups_requested

Detailed Description

Communication between colvars and NAMD (implementation of colvarproxy)

Definition at line 39 of file colvarproxy_namd.h.

Constructor & Destructor Documentation

◆ colvarproxy_namd()

colvarproxy_namd::colvarproxy_namd ( )

Definition at line 46 of file colvarproxy_namd.C.

References accelMDOn, SimParameters::accelMDOn, amd_weight_factor, COLVARPROXY_VERSION, Node::colvars, Node::configList, StringList::data, debug, SimParameters::dt, endi(), error(), ConfigList::find(), first_timestep, SimParameters::firstTimestep, GLOBAL_MASTER_CKLOOP_CALC_BIASES, GLOBAL_MASTER_CKLOOP_CALC_ITEM, GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES, init_atoms_map(), iout, StringList::next, Node::Object(), ReductionMgr::Object(), SimParameters::outputFilename, random, SimParameters::randomSeed, PatchData::reduction, REDUCTIONS_BASIC, GlobalMaster::requestTotalForce(), SimParameters::restartFilename, SimParameters::restartFrequency, setup(), Node::simParameters, simparams, update_target_temperature(), and ReductionMgr::willSubmit().

 {
   engine_name_ = "NAMD";
 #if CMK_SMP && USE_CKLOOP
   charm_lock_state = CmiCreateLock();
 #endif
 
   version_int = get_version_from_string(COLVARPROXY_VERSION);
 #if CMK_TRACE_ENABLED
   if ( 0 == CkMyPe() ) {
     traceRegisterUserEvent("GM COLVAR item", GLOBAL_MASTER_CKLOOP_CALC_ITEM);
     traceRegisterUserEvent("GM COLVAR bias", GLOBAL_MASTER_CKLOOP_CALC_BIASES );
     traceRegisterUserEvent("GM COLVAR scripted bias", GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES );
   }
 #endif
   first_timestep = true;
   requestTotalForce(total_force_requested);
 
   boltzmann_ = 0.001987191;
 
   angstrom_value_ = 1.;
 
   // initialize pointers to NAMD configuration data
   simparams = Node::Object()->simParameters;
 
   if (cvm::debug())
     iout << "Info: initializing the colvars proxy object.\n" << endi;
 
   // find the configuration file, if provided
   StringList *config = Node::Object()->configList->find("colvarsConfig");
 
   // find the input state file
   StringList *input_restart = Node::Object()->configList->find("colvarsInput");
   colvarproxy_io::set_input_prefix(input_restart ? input_restart->data : "");
 
   update_target_temperature();
   set_integration_timestep(simparams->dt);
 
   random = Random(simparams->randomSeed);
 
   // both fields are taken from data structures already available
   updated_masses_ = updated_charges_ = true;
 
   // Take the output prefixes from the NAMD input
   colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename));
   colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename));
   colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency);
 
   if (simparams->accelMDOn) {
     accelMDOn = true;
   } else {
     accelMDOn = false;
   }
   amd_weight_factor = 1.0;
 
   // check if it is possible to save output configuration
   if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
     error("Error: neither the final output state file or "
           "the output restart file could be defined, exiting.\n");
   }
 
   init_atoms_map();
 
   // initialize module: this object will be the communication proxy
   colvars = new colvarmodule(this);
 
   cvm::log("Using NAMD interface, version "+
            cvm::to_str(COLVARPROXY_VERSION)+".\n");
   colvars->cite_feature("NAMD engine");
   colvars->cite_feature("Colvars-NAMD interface");
 
   errno = 0;
   for ( ; config; config = config->next ) {
     add_config("configfile", config->data);
   }
 
   // Trigger immediate initialization of the module
   colvarproxy::parse_module_config();
   colvarproxy_namd::setup();
   colvars->update_engine_parameters();
   colvars->setup_input();
   colvars->setup_output();
 
   // save to Node for Tcl script access
   Node::Object()->colvars = colvars;
 
 #ifdef NAMD_TCL
   have_scripts = true;
 #else
   have_scripts = false;
 #endif
 
   if (simparams->firstTimestep != 0) {
     colvars->set_initial_step(static_cast<cvm::step_number>(simparams->firstTimestep));
   }
 
 #if !defined (NAMD_UNIFIED_REDUCTION)
   reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);
 #endif
 
   #if defined(NODEGROUP_FORCE_REGISTER) && !defined(NAMD_UNIFIED_REDUCTION)
   CProxy_PatchData cpdata(CkpvAccess(BOCclass_group).patchData);
   PatchData *patchData = cpdata.ckLocalBranch();
   nodeReduction = patchData->reduction;
   #endif
 
   if (cvm::debug())
     iout << "Info: done initializing the colvars proxy object.\n" << endi;
 }

◆ ~colvarproxy_namd()

colvarproxy_namd::~colvarproxy_namd ( )

Definition at line 157 of file colvarproxy_namd.C.

 {
 #if CMK_SMP && USE_CKLOOP
   CmiDestroyLock(charm_lock_state);
 #endif
 #if !defined (NAMD_UNIFIED_REDUCTION)
   delete reduction;
 #endif
 }

Member Function Documentation

◆ accelMD_enabled()

bool colvarproxy_namd::accelMD_enabled ( ) const

inlineoverride

Definition at line 124 of file colvarproxy_namd.h.

References accelMDOn.

                                         {
     return accelMDOn;
   }

◆ add_energy()

void colvarproxy_namd::add_energy ( cvm::real energy )

override

Definition at line 663 of file colvarproxy_namd.C.

References GlobalMaster::addReductionEnergy(), SimParameters::CUDASOAintegrate, REDUCTION_MISC_ENERGY, and simparams.

 {
   #if defined(NODEGROUP_FORCE_REGISTER) && !defined(NAMD_UNIFIED_REDUCTION)
   if (simparams->CUDASOAintegrate) {
     nodeReduction->item(REDUCTION_MISC_ENERGY) += energy;
   } else {
     reduction->item(REDUCTION_MISC_ENERGY) += energy;
   }
   #else
   #if !defined(NAMD_UNIFIED_REDUCTION)
   reduction->item(REDUCTION_MISC_ENERGY) += energy;
   #else
   addReductionEnergy(REDUCTION_MISC_ENERGY, energy);
   #endif
   #endif
 }

◆ backup_file()

int colvarproxy_namd::backup_file ( char const * filename )

override

Definition at line 1188 of file colvarproxy_namd.C.

References NAMD_backup_file().

Referenced by output_stream().

 {
   if (std::string(filename).rfind(std::string(".colvars.state")) != std::string::npos) {
     NAMD_backup_file(filename, ".old");
   } else {
     NAMD_backup_file(filename, ".BAK");
   }
   return COLVARS_OK;
 }

◆ calculate()

void colvarproxy_namd::calculate ( )

virtual

Reimplemented from GlobalMaster.

Definition at line 345 of file colvarproxy_namd.C.

 {
   errno = 0;
 
   if (first_timestep) {
 
     // First run after the proxy is constructed
 
     colvarproxy_namd::setup();
     colvars->update_engine_parameters();
     colvars->setup_input();
     colvars->setup_output();
     // Controller is only available after full startup phase, so now
     controller = &Node::Object()->state->getController();
 
     first_timestep = false;
 
   } else {
 
     // Use the time step number inherited from GlobalMaster
     if ( step - previous_NAMD_step == 1 ) {
       colvars->it++;
       b_simulation_continuing = false;
     } else {
 
       // Cases covered by this condition:
       // - run 0
       // - beginning of a new run statement
       // The internal counter is not incremented, and the objects are made
       // aware of this via the following flag
       b_simulation_continuing = true;
 
       // Update NAMD output and restart prefixes
       colvarproxy_io::set_output_prefix(std::string(simparams->outputFilename));
       colvarproxy_io::set_restart_output_prefix(std::string(simparams->restartFilename));
       colvarproxy_io::set_default_restart_frequency(simparams->restartFrequency);
       colvars->setup_output();
 
     }
   }
 
   previous_NAMD_step = step;
   if (accelMDOn) update_accelMD_info();
 
   {
     Vector const a = lattice->a();
     Vector const b = lattice->b();
     Vector const c = lattice->c();
     unit_cell_x.set(a.x, a.y, a.z);
     unit_cell_y.set(b.x, b.y, c.z);
     unit_cell_z.set(c.x, c.y, c.z);
   }
 
   if (!lattice->a_p() && !lattice->b_p() && !lattice->c_p()) {
     boundaries_type = boundaries_non_periodic;
     reset_pbc_lattice();
   } else if (lattice->a_p() && lattice->b_p() && lattice->c_p()) {
     if (lattice->orthogonal()) {
       boundaries_type = boundaries_pbc_ortho;
     } else {
       boundaries_type = boundaries_pbc_triclinic;
     }
     colvarproxy_system::update_pbc_lattice();
   } else {
     boundaries_type = boundaries_unsupported;
   }
 
   if (cvm::debug()) {
     cvm::log(std::string(cvm::line_marker)+
              "colvarproxy_namd, step no. "+cvm::to_str(colvars->it)+"\n"+
              "Updating atomic data arrays.\n");
   }
 
   // must delete the forces applied at the previous step: we can do
   // that because they have already been used and copied to other
   // memory locations
   modifyForcedAtoms().clear();
   modifyAppliedForces().clear();
 
   // If new atomic positions or forces have been requested by other
   // GlobalMaster objects, add these to the atom map as well
   size_t const n_all_atoms = Node::Object()->molecule->numAtoms;
   if ( (atoms_map.size() != n_all_atoms) ||
        (int(atoms_ids.size()) < (getAtomIdEnd() - getAtomIdBegin())) ||
        (int(atoms_ids.size()) < (getForceIdEnd() - getForceIdBegin())) ) {
     update_atoms_map(getAtomIdBegin(), getAtomIdEnd());
     update_atoms_map(getForceIdBegin(), getForceIdEnd());
   }
 
   // prepare local arrays
   for (size_t i = 0; i < atoms_ids.size(); i++) {
     atoms_positions[i] = cvm::rvector(0.0, 0.0, 0.0);
     atoms_total_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
     atoms_new_colvar_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
   }
 
   for (size_t i = 0; i < atom_groups_ids.size(); i++) {
     atom_groups_total_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
     atom_groups_new_colvar_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
   }
 
 #if NAMD_VERSION_NUMBER >= 34471681
   for (int imap = 0; imap < volmaps_ids.size(); imap++) {
     volmaps_new_colvar_forces[imap] = 0.0;
   }
 #endif
 
   {
     if (cvm::debug()) {
       cvm::log("Updating positions arrays.\n");
     }
     size_t n_positions = 0;
     AtomIDList::const_iterator a_i = getAtomIdBegin();
     AtomIDList::const_iterator a_e = getAtomIdEnd();
     PositionList::const_iterator p_i = getAtomPositionBegin();
 
     for ( ; a_i != a_e; ++a_i, ++p_i ) {
       atoms_positions[atoms_map[*a_i]] = cvm::rvector((*p_i).x, (*p_i).y, (*p_i).z);
       n_positions++;
     }
 
     // The following had to be relaxed because some atoms may be forced without their position being requested
     // if (n_positions < atoms_ids.size()) {
     //   cvm::error("Error: did not receive the positions of all atoms.\n", COLVARS_BUG_ERROR);
     // }
   }
 
   if (total_force_requested && cvm::step_relative() > 0) {
 
     // sort the force arrays the previous step
     // (but only do so if there *is* a previous step!)
 
     {
       if (cvm::debug()) {
         cvm::log("Updating total forces arrays.\n");
       }
       size_t n_total_forces = 0;
       AtomIDList::const_iterator a_i = getForceIdBegin();
       AtomIDList::const_iterator a_e = getForceIdEnd();
       ForceList::const_iterator f_i = getTotalForce();
 
       for ( ; a_i != a_e; ++a_i, ++f_i ) {
         atoms_total_forces[atoms_map[*a_i]] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);
         n_total_forces++;
       }
 
       if ( (! b_simulation_continuing) &&
            (n_total_forces < atoms_ids.size()) ) {
         cvm::error("Error: total forces were requested, but total forces "
                    "were not received for all atoms.\n"
                    "The most probable cause is combination of energy "
                    "minimization with a biasing method that requires MD (e.g. ABF).\n"
                    "Always run minimization and ABF separately.", COLVARS_INPUT_ERROR);
       }
     }
 
     {
       if (cvm::debug()) {
         cvm::log("Updating group total forces arrays.\n");
       }
       ForceList::const_iterator f_i = getGroupTotalForceBegin();
       ForceList::const_iterator f_e = getGroupTotalForceEnd();
       size_t i = 0;
       if ( (! b_simulation_continuing) &&
            ((f_e - f_i) != ((int) atom_groups_ids.size())) ) {
         cvm::error("Error: total forces were requested for scalable groups, "
                    "but they are not in the same number from the number of groups.\n"
                    "The most probable cause is combination of energy "
                    "minimization with a biasing method that requires MD (e.g. ABF).\n"
                    "Always run minimization and ABF separately.", COLVARS_INPUT_ERROR);
       }
       for ( ; f_i != f_e; f_i++, i++) {
         atom_groups_total_forces[i] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);
       }
     }
   }
 
   {
     if (cvm::debug()) {
       cvm::log("Updating group positions arrays.\n");
     }
     // update group data (only coms available so far)
     size_t ig;
     // note: getGroupMassBegin() could be used here, but masses and charges
     // have already been calculated from the last call to setup()
     PositionList::const_iterator gp_i = getGroupPositionBegin();
     for (ig = 0; gp_i != getGroupPositionEnd(); gp_i++, ig++) {
       atom_groups_coms[ig] = cvm::rvector(gp_i->x, gp_i->y, gp_i->z);
     }
   }
 
 #if NAMD_VERSION_NUMBER >= 34471681
   {
     if (cvm::debug()) {
       log("Updating grid objects.\n");
     }
     // Using a simple nested loop: there probably won't be so many maps that
     // this becomes performance-limiting
     IntList::const_iterator goi_i = getGridObjIndexBegin();
     BigRealList::const_iterator gov_i = getGridObjValueBegin();
     for ( ; gov_i != getGridObjValueEnd(); goi_i++, gov_i++) {
       for (size_t imap = 0; imap < volmaps_ids.size(); imap++) {
         if (volmaps_ids[imap] == *goi_i) {
           volmaps_values[imap] = *gov_i;
           break;
         }
       }
     }
   }
 #endif
 
   if (cvm::debug()) {
     print_input_atomic_data();
   }
 
   // call the collective variable module
   if (colvars->calc() != COLVARS_OK) {
     cvm::error("Error in the collective variables module.\n", COLVARS_ERROR);
   }
 
   if (cvm::debug()) {
     print_output_atomic_data();
   }
 
   // communicate all forces to the MD integrator
   for (size_t i = 0; i < atoms_ids.size(); i++) {
     cvm::rvector const &f = atoms_new_colvar_forces[i];
     modifyForcedAtoms().add(atoms_ids[i]);
     modifyAppliedForces().add(Vector(f.x, f.y, f.z));
   }
 
   if (atom_groups_new_colvar_forces.size() > 0) {
     modifyGroupForces().resize(requestedGroups().size());
     ForceList::iterator gf_i = modifyGroupForces().begin();
     for (int ig = 0; gf_i != modifyGroupForces().end(); gf_i++, ig++) {
       cvm::rvector const &f = atom_groups_new_colvar_forces[ig];
       *gf_i = Vector(f.x, f.y, f.z);
     }
   }
 
 #if NAMD_VERSION_NUMBER >= 34471681
   if (volmaps_new_colvar_forces.size() > 0) {
     modifyGridObjForces().resize(requestedGridObjs().size());
     modifyGridObjForces().setall(0.0);
     IntList::const_iterator goi_i = getGridObjIndexBegin();
     BigRealList::iterator gof_i = modifyGridObjForces().begin();
     for ( ; goi_i != getGridObjIndexEnd(); goi_i++, gof_i++) {
       for (size_t imap = 0; imap < volmaps_ids.size(); imap++) {
         if (volmaps_ids[imap] == *goi_i) {
           *gof_i = volmaps_new_colvar_forces[imap];
           break;
         }
       }
     }
   }
 #endif
 
   // send MISC energy
   #if defined(NODEGROUP_FORCE_REGISTER) && !defined(NAMD_UNIFIED_REDUCTION)
   if(!simparams->CUDASOAintegrate) {
     reduction->submit();
   }
   #else
   #if !defined(NAMD_UNIFIED_REDUCTION)
   reduction->submit();
   #else
   // submitReduction();
   #endif
   #endif
 
   // NAMD does not destruct GlobalMaster objects, so we must remember
   // to write all output files at the end of a run
   if (step == simparams->N) {
     post_run();
   }
 }

◆ check_atom_id() [1/2]

int colvarproxy_namd::check_atom_id ( int atom_number )

override

Definition at line 724 of file colvarproxy_namd.C.

References debug, Node::molecule, Molecule::numAtoms, and Node::Object().

Referenced by init_atom().

 {
   // NAMD's internal numbering starts from zero
   int const aid = (atom_number-1);
 
   if (cvm::debug())
     cvm::log("Adding atom "+cvm::to_str(atom_number)+
         " for collective variables calculation.\n");
 
   if ( (aid < 0) || (aid >= Node::Object()->molecule->numAtoms) ) {
     cvm::error("Error: invalid atom number specified, "+
                cvm::to_str(atom_number)+"\n", COLVARS_INPUT_ERROR);
     return COLVARS_INPUT_ERROR;
   }
 
   return aid;
 }

◆ check_atom_id() [2/2]

int colvarproxy_namd::check_atom_id	(	cvm::residue_id const &	residue,
		std::string const &	atom_name,
		std::string const &	segment_id
	)

override

Definition at line 777 of file colvarproxy_namd.C.

References Molecule::get_atom_from_name(), Node::molecule, and Node::Object().

 {
   int const aid =
     (segment_id.size() ?
      Node::Object()->molecule->get_atom_from_name(segment_id.c_str(),
                                                   residue,
                                                   atom_name.c_str()) :
      Node::Object()->molecule->get_atom_from_name("MAIN",
                                                   residue,
                                                   atom_name.c_str()));
 
   if (aid < 0) {
     // get_atom_from_name() has returned an error value
     cvm::error("Error: could not find atom \""+
                atom_name+"\" in residue "+
                cvm::to_str(residue)+
                ( (segment_id != "MAIN") ?
                  (", segment \""+segment_id+"\"") :
                  ("") )+
                "\n", COLVARS_INPUT_ERROR);
     return COLVARS_INPUT_ERROR;
   }
 
   return aid;
 }

◆ check_atom_name_selections_available()

int colvarproxy_namd::check_atom_name_selections_available ( )

override

Definition at line 743 of file colvarproxy_namd.C.

 {
   return COLVARS_OK;
 }

◆ check_replicas_enabled()

int colvarproxy_namd::check_replicas_enabled ( )

override

Definition at line 1614 of file colvarproxy_namd.C.

                                              {
 #if CMK_HAS_PARTITION
   return COLVARS_OK;
 #else
   return COLVARS_NOT_IMPLEMENTED;
 #endif
 }

◆ check_volmap_by_id()

int colvarproxy_namd::check_volmap_by_id ( int volmap_id )

override

Definition at line 1387 of file colvarproxy_namd.C.

References Node::molecule, Molecule::numGridforceGrids, and Node::Object().

Referenced by init_volmap_by_id().

 {
   Molecule *mol = Node::Object()->molecule;
   if ((volmap_id < 0) || (volmap_id >= mol->numGridforceGrids)) {
     return cvm::error("Error: invalid numeric ID ("+cvm::to_str(volmap_id)+
                       ") for map.\n", COLVARS_INPUT_ERROR);
   }
   colvars->cite_feature("GridForces volumetric map implementation for NAMD");
   return COLVARS_OK;
 }

◆ check_volmap_by_name()

int colvarproxy_namd::check_volmap_by_name ( char const * volmap_name )

override

Definition at line 1399 of file colvarproxy_namd.C.

References MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, and simparams.

Referenced by get_volmap_id_from_name(), and init_volmap_by_name().

 {
   if (volmap_name == NULL) {
     return cvm::error("Error: no grid object name provided.", COLVARS_INPUT_ERROR);
   }
   int volmap_id = simparams->mgridforcelist.index_for_key(volmap_name);
   if (volmap_id < 0) {
     return cvm::error("Error: invalid map name \""+std::string(volmap_name)+
                       "\".\n", COLVARS_INPUT_ERROR);
   }
   colvars->cite_feature("GridForces volumetric map implementation for NAMD");
   return COLVARS_OK;
 }

◆ check_volmaps_available()

int colvarproxy_namd::check_volmaps_available ( )

override

Definition at line 1318 of file colvarproxy_namd.C.

 {
   return COLVARS_OK;
 }

◆ clear_atom()

void colvarproxy_namd::clear_atom ( int index )

override

Definition at line 839 of file colvarproxy_namd.C.

 {
   colvarproxy::clear_atom(index);
   // TODO remove it from GlobalMaster arrays?
 }

◆ clear_atom_group()

void colvarproxy_namd::clear_atom_group ( int index )

override

Definition at line 1271 of file colvarproxy_namd.C.

 {
   // do nothing, keep the NAMD arrays in sync with the colvarproxy ones
   colvarproxy::clear_atom_group(index);
 }

◆ clear_volmap()

void colvarproxy_namd::clear_volmap ( int index )

override

Definition at line 1414 of file colvarproxy_namd.C.

 {
   // TODO remove from GlobalMaster
   colvarproxy::clear_volmap(index);
 }

◆ close_output_stream()

int colvarproxy_namd::close_output_stream ( std::string const & output_name )

override

Definition at line 1154 of file colvarproxy_namd.C.

 {
   if (!io_available()) {
     return cvm::error("Error: trying to access an output file/channel "
                       "from the wrong thread.\n", COLVARS_BUG_ERROR);
   }
 
   if (output_streams_.count(output_name) > 0) {
     (reinterpret_cast<ofstream_namd *>(output_streams_[output_name]))->close();
     delete output_streams_[output_name];
     output_streams_.erase(output_name);
   }
 
   return COLVARS_OK;
 }

◆ close_output_streams()

int colvarproxy_namd::close_output_streams ( )

override

Definition at line 1171 of file colvarproxy_namd.C.

 {
   if (! io_available()) {
     return COLVARS_OK;
   }
 
   for (std::map<std::string, std::ostream *>::iterator osi = output_streams_.begin();
        osi != output_streams_.end();
        osi++) {
     (reinterpret_cast<ofstream_namd *>(osi->second))->close();
   }
   output_streams_.clear();
 
   return COLVARS_OK;
 }

◆ compute_volmap()

int colvarproxy_namd::compute_volmap	(	int	flags,
		int	volmap_id,
		cvm::atom_iter	atom_begin,
		cvm::atom_iter	atom_end,
		cvm::real *	value,
		cvm::real *	atom_field
	)

override

Definition at line 1486 of file colvarproxy_namd.C.

References GridforceGrid::get_grid_type(), Molecule::get_gridfrc_grid(), GridforceGrid::GridforceGridTypeFull, GridforceGrid::GridforceGridTypeLite, Node::molecule, and Node::Object().

 {
   Molecule *mol = Node::Object()->molecule;
   GridforceGrid *grid = mol->get_gridfrc_grid(volmap_id);
   // Inheritance is not possible with GridForceGrid's design
   if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeFull) {
     GridforceFullMainGrid *g = dynamic_cast<GridforceFullMainGrid *>(grid);
     getGridForceGridValue<GridforceFullMainGrid>(flags, g, atom_begin, atom_end,
                                                  value, atom_field);
   } else if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeLite) {
     GridforceLiteGrid *g = dynamic_cast<GridforceLiteGrid *>(grid);
     getGridForceGridValue<GridforceLiteGrid>(flags, g, atom_begin, atom_end,
                                              value, atom_field);
   }
   return COLVARS_OK;
 }

◆ error()

void colvarproxy_namd::error ( std::string const & message )

override

Definition at line 703 of file colvarproxy_namd.C.

References log(), NAMD_die(), and NAMD_err().

Referenced by colvarproxy_namd().

 {
   log(message);
   switch (cvm::get_error()) {
   case COLVARS_FILE_ERROR:
     errno = EIO; break;
   case COLVARS_NOT_IMPLEMENTED:
     errno = ENOSYS; break;
   case COLVARS_MEMORY_ERROR:
     errno = ENOMEM; break;
   }
   char const *msg = "Error in the collective variables module "
     "(see above for details)";
   if (errno) {
     NAMD_err(msg);
   } else {
     NAMD_die(msg);
   }
 }

◆ flush_output_stream()

int colvarproxy_namd::flush_output_stream ( std::string const & output_name )

override

Definition at line 1122 of file colvarproxy_namd.C.

 {
   if (!io_available()) {
     return COLVARS_OK;
   }
 
   if (output_streams_.count(output_name) > 0) {
     (reinterpret_cast<ofstream_namd *>(output_streams_[output_name]))->flush();
     return COLVARS_OK;
   }
 
   return cvm::error("Error: trying to flush an output file/channel "
                     "that wasn't open.\n", COLVARS_BUG_ERROR);
 }

◆ flush_output_streams()

int colvarproxy_namd::flush_output_streams ( )

override

Definition at line 1138 of file colvarproxy_namd.C.

 {
   if (!io_available()) {
     return COLVARS_OK;
   }
 
   for (std::map<std::string, std::ostream *>::iterator osi = output_streams_.begin();
        osi != output_streams_.end();
        osi++) {
     (reinterpret_cast<ofstream_namd *>(osi->second))->flush();
   }
 
   return COLVARS_OK;
 }

◆ get_accelMD_factor()

cvm::real colvarproxy_namd::get_accelMD_factor ( ) const

inlineoverride

Definition at line 120 of file colvarproxy_namd.h.

References amd_weight_factor.

                                               {
     return amd_weight_factor;
   }

◆ get_alch_lambda()

int colvarproxy_namd::get_alch_lambda ( cvm::real * lambda )

Get value of alchemical lambda parameter from back-end.

Definition at line 1681 of file colvarproxy_namd.C.

References SimParameters::getCurrentLambda(), simparams, and GlobalMaster::step.

                                                      {
   *lambda = simparams->getCurrentLambda(step);
   return COLVARS_OK;
 }

◆ get_dE_dlambda()

int colvarproxy_namd::get_dE_dlambda ( cvm::real * dE_dlambda )

Get energy derivative with respect to lambda.

Definition at line 1702 of file colvarproxy_namd.C.

References controller, and Controller::getTIderivative().

                                                         {
   // Force data at step zero is garbage in NAMD3, zero in NAMD2
   if (cvm::step_relative() > 0) {
     *dE_dlambda = controller->getTIderivative();
   } else {
     *dE_dlambda = 0.0;
   }
   return COLVARS_OK;
 }

◆ get_volmap_id_from_name()

int colvarproxy_namd::get_volmap_id_from_name ( char const * volmap_name )

override

Definition at line 1421 of file colvarproxy_namd.C.

References check_volmap_by_name(), MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, and simparams.

 {
   int const volmap_id =
     simparams->mgridforcelist.index_for_key(volmap_name);
   if (volmap_id < 0) {
     // Print error
     check_volmap_by_name(volmap_name);
   }
   return volmap_id;
 }

◆ getGridForceGridValue()

template<class T >

void colvarproxy_namd::getGridForceGridValue	(	int	flags,
		T const *	grid,
		cvm::atom_iter	atom_begin,
		cvm::atom_iter	atom_end,
		cvm::real *	value,
		cvm::real *	atom_field
	)

Abstraction of the two types of NAMD volumetric maps.

Definition at line 1467 of file colvarproxy_namd.C.

 {
   if (flags & volmap_flag_use_atom_field) {
     int const new_flags = volmap_flag_use_atom_field | volmap_flag_gradients;
     GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end,
                                     value, atom_field);
   } else {
     int const new_flags = volmap_flag_gradients;
     GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end,
                                     value, atom_field);
   }
 }

◆ GridForceGridLoop()

template<class T , int flags>

void colvarproxy_namd::GridForceGridLoop	(	T const *	g,
		cvm::atom_iter	atom_begin,
		cvm::atom_iter	atom_end,
		cvm::real *	value,
		cvm::real *	atom_field
	)

Implementation of inner loop; allows for atom list computation and use.

Definition at line 1434 of file colvarproxy_namd.C.

References Vector::x, Vector::y, and Vector::z.

 {
   float V = 0.0f;
   Vector dV(0.0);
   int i = 0;
   cvm::atom_iter ai = atom_begin;
   for ( ; ai != atom_end; ai++, i++) {
     if (g->compute_VdV(Position(ai->pos.x, ai->pos.y, ai->pos.z), V, dV)) {
       // out-of-bounds atom
       V = 0.0f;
       dV = 0.0;
     } else {
       if (flags & volmap_flag_use_atom_field) {
         *value += V * atom_field[i];
         if (flags & volmap_flag_gradients) {
           ai->grad += atom_field[i] * cvm::rvector(dV.x, dV.y, dV.z);
         }
       } else {
         *value += V;
         if (flags & volmap_flag_gradients) {
           ai->grad += cvm::rvector(dV.x, dV.y, dV.z);
         }
       }
     }
   }
 }

◆ init_atom() [1/2]

int colvarproxy_namd::init_atom ( int atom_number )

override

Definition at line 749 of file colvarproxy_namd.C.

References ResizeArray< Elem >::add(), atoms_map, check_atom_id(), GlobalMaster::modifyRequestedAtoms(), and update_atom_properties().

 {
   // save time by checking first whether this atom has been requested before
   // (this is more common than a non-valid atom number)
   int aid = (atom_number-1);
 
   for (size_t i = 0; i < atoms_ids.size(); i++) {
     if (atoms_ids[i] == aid) {
       // this atom id was already recorded
       atoms_refcount[i] += 1;
       return i;
     }
   }
 
   aid = check_atom_id(atom_number);
 
   if (aid < 0) {
     return COLVARS_INPUT_ERROR;
   }
 
   int const index = add_atom_slot(aid);
   atoms_map[aid] = index;
   modifyRequestedAtoms().add(aid);
   update_atom_properties(index);
   return index;
 }

◆ init_atom() [2/2]

int colvarproxy_namd::init_atom	(	cvm::residue_id const &	residue,
		std::string const &	atom_name,
		std::string const &	segment_id
	)

override

For AMBER topologies, the segment id is automatically set to "MAIN" (the segment id assigned by NAMD's AMBER topology parser), and is therefore optional when an AMBER topology is used

Definition at line 810 of file colvarproxy_namd.C.

References ResizeArray< Elem >::add(), atoms_map, check_atom_id(), debug, GlobalMaster::modifyRequestedAtoms(), and update_atom_properties().

 {
   int const aid = check_atom_id(residue, atom_name, segment_id);
 
   for (size_t i = 0; i < atoms_ids.size(); i++) {
     if (atoms_ids[i] == aid) {
       // this atom id was already recorded
       atoms_refcount[i] += 1;
       return i;
     }
   }
 
   if (cvm::debug())
     cvm::log("Adding atom \""+
         atom_name+"\" in residue "+
         cvm::to_str(residue)+
         " (index "+cvm::to_str(aid)+
         ") for collective variables calculation.\n");
 
   int const index = add_atom_slot(aid);
   atoms_map[aid] = index;
   modifyRequestedAtoms().add(aid);
   update_atom_properties(index);
   return index;
 }

◆ init_atom_group()

int colvarproxy_namd::init_atom_group ( std::vector< int > const & atoms_ids )

override

Definition at line 1199 of file colvarproxy_namd.C.

References debug, GlobalMaster::modifyGroupForces(), GlobalMaster::modifyRequestedGroups(), Node::molecule, Molecule::numAtoms, Node::Object(), ResizeArray< Elem >::resize(), ResizeArray< Elem >::size(), and update_group_properties().

 {
   if (cvm::debug())
     cvm::log("Requesting from NAMD a group of size "+cvm::to_str(atoms_ids.size())+
         " for collective variables calculation.\n");
 
   colvars->cite_feature("Scalable center-of-mass computation (NAMD)");
 
   // Note: modifyRequestedGroups is supposed to be in sync with the colvarproxy arrays,
   // and to stay that way during a simulation
 
   // compare this new group to those already allocated inside GlobalMaster
   int ig;
   for (ig = 0; ig < modifyRequestedGroups().size(); ig++) {
     AtomIDList const &namd_group = modifyRequestedGroups()[ig];
     bool b_match = true;
 
     if (namd_group.size() != ((int) atoms_ids.size())) {
       b_match = false;
     } else {
       int ia;
       for (ia = 0; ia < namd_group.size(); ia++) {
         int const aid = atoms_ids[ia];
         if (namd_group[ia] != aid) {
           b_match = false;
           break;
         }
       }
     }
 
     if (b_match) {
       if (cvm::debug())
         cvm::log("Group was already added.\n");
       // this group already exists
       atom_groups_refcount[ig] += 1;
       return ig;
     }
   }
 
   // add this group (note: the argument of add_atom_group_slot() is redundant for NAMD, and provided only for consistency)
   size_t const index = add_atom_group_slot(atom_groups_ids.size());
   modifyRequestedGroups().resize(atom_groups_ids.size());
   // the following is done in calculate()
   // modifyGroupForces().resize(atom_groups_ids.size());
   AtomIDList &namd_group = modifyRequestedGroups()[index];
   namd_group.resize(atoms_ids.size());
   int const n_all_atoms = Node::Object()->molecule->numAtoms;
   for (size_t ia = 0; ia < atoms_ids.size(); ia++) {
     int const aid = atoms_ids[ia];
     if (cvm::debug())
       cvm::log("Adding atom "+cvm::to_str(aid+1)+
           " for collective variables calculation.\n");
     if ( (aid < 0) || (aid >= n_all_atoms) ) {
       cvm::error("Error: invalid atom number specified, "+
                  cvm::to_str(aid+1)+"\n", COLVARS_INPUT_ERROR);
       return -1;
     }
     namd_group[ia] = aid;
   }
 
   update_group_properties(index);
 
   if (cvm::debug()) {
     cvm::log("Group has index "+cvm::to_str(index)+"\n");
     cvm::log("modifyRequestedGroups length = "+cvm::to_str(modifyRequestedGroups().size())+
         ", modifyGroupForces length = "+cvm::to_str(modifyGroupForces().size())+"\n");
   }
 
   return index;
 }

◆ init_atoms_map()

void colvarproxy_namd::init_atoms_map ( )

Allocate an atoms map with the same size as the NAMD topology.

Definition at line 191 of file colvarproxy_namd.C.

References atoms_map, Node::molecule, Molecule::numAtoms, and Node::Object().

Referenced by colvarproxy_namd(), and update_atoms_map().

 {
   size_t const n_all_atoms = Node::Object()->molecule->numAtoms;
   atoms_map.assign(n_all_atoms, -1);
 }

◆ init_tcl_pointers()

void colvarproxy_namd::init_tcl_pointers ( )

override

Definition at line 630 of file colvarproxy_namd.C.

References Node::Object().

 {
 #ifdef NAMD_TCL
   // Store pointer to NAMD's Tcl interpreter
   set_tcl_interp(Node::Object()->getScript()->interp);
 #else
   colvarproxy::init_tcl_pointers(); // Create dedicated interpreter
 #endif
 }

◆ init_volmap_by_id()

int colvarproxy_namd::init_volmap_by_id ( int volmap_id )

override

Definition at line 1324 of file colvarproxy_namd.C.

References ResizeArray< Elem >::add(), check_volmap_by_id(), and GlobalMaster::modifyRequestedGridObjects().

 {
   for (size_t i = 0; i < volmaps_ids.size(); i++) {
     if (volmaps_ids[i] == volmap_id) {
       // this map has already been requested
       volmaps_refcount[i] += 1;
       return i;
     }
   }
 
   int error_code = check_volmap_by_id(volmap_id);
   int index = -1;
   if (error_code == COLVARS_OK) {
     index = add_volmap_slot(volmap_id);
     modifyRequestedGridObjects().add(volmap_id);
   }
 
   return (error_code == COLVARS_OK) ? index : -1;
 }

◆ init_volmap_by_name()

int colvarproxy_namd::init_volmap_by_name ( const char * volmap_name )

override

Definition at line 1345 of file colvarproxy_namd.C.

References ResizeArray< Elem >::add(), check_volmap_by_name(), Molecule::get_gridfrc_grid(), GridforceGrid::get_scale(), MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, GlobalMaster::modifyRequestedGridObjects(), Node::molecule, Node::Object(), simparams, Vector::x, Vector::y, and Vector::z.

 {
   if (volmap_name == NULL) {
     return cvm::error("Error: no grid object name provided.", COLVARS_INPUT_ERROR);
   }
 
   int error_code = COLVARS_OK;
 
   error_code |= check_volmap_by_name(volmap_name);
 
   int index = -1;
   if (error_code == COLVARS_OK) {
 
     int volmap_id = simparams->mgridforcelist.index_for_key(volmap_name);
 
     // Check that the scale factor is correctly set to zero
     Molecule *mol = Node::Object()->molecule;
     GridforceGrid const *grid = mol->get_gridfrc_grid(volmap_id);
     Vector const gfScale = grid->get_scale();
     if ((gfScale.x != 0.0) || (gfScale.y != 0.0) || (gfScale.z != 0.0)) {
       error_code |= cvm::error("Error: GridForce map \""+
                                std::string(volmap_name)+
                                "\" has non-zero scale factors.\n",
                                COLVARS_INPUT_ERROR);
     }
 
     for (size_t i = 0; i < volmaps_ids.size(); i++) {
       if (volmaps_ids[i] == volmap_id) {
         // this map has already been requested
         volmaps_refcount[i] += 1;
         return i;
       }
     }
 
     index = add_volmap_slot(volmap_id);
     modifyRequestedGridObjects().add(volmap_id);
   }
 
   return (error_code == COLVARS_OK) ? index : -1;
 }

◆ load_atoms_pdb()

int colvarproxy_namd::load_atoms_pdb	(	char const *	filename,
		cvm::atom_group &	atoms,
		std::string const &	pdb_field,
		double const	pdb_field_value
	)

override

Definition at line 1036 of file colvarproxy_namd.C.

References PDB::atom(), cvm::atom, e_pdb_beta, e_pdb_occ, e_pdb_x, e_pdb_y, e_pdb_z, PDB::num_atoms(), and pdb_field_str2enum().

 {
   if (pdb_field_str.size() == 0)
     cvm::error("Error: must define which PDB field to use "
                "in order to define atoms from a PDB file.\n", COLVARS_INPUT_ERROR);
 
   PDB *pdb = new PDB(pdb_filename);
   size_t const pdb_natoms = pdb->num_atoms();
 
   e_pdb_field pdb_field_index = pdb_field_str2enum(pdb_field_str);
 
   for (size_t ipdb = 0; ipdb < pdb_natoms; ipdb++) {
 
     double atom_pdb_field_value = 0.0;
 
     switch (pdb_field_index) {
     case e_pdb_occ:
       atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
       break;
     case e_pdb_beta:
       atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
       break;
     case e_pdb_x:
       atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
       break;
     case e_pdb_y:
       atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
       break;
     case e_pdb_z:
       atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
       break;
     default:
       break;
     }
 
     if ( (pdb_field_value) &&
          (atom_pdb_field_value != pdb_field_value) ) {
       continue;
     } else if (atom_pdb_field_value == 0.0) {
       continue;
     }
 
     if (atoms.is_enabled(colvardeps::f_ag_scalable)) {
       atoms.add_atom_id(ipdb);
     } else {
       atoms.add_atom(cvm::atom(ipdb+1));
     }
   }
 
   delete pdb;
   return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
 }

◆ load_coords_pdb()

int colvarproxy_namd::load_coords_pdb	(	char const *	filename,
		std::vector< cvm::atom_pos > &	pos,
		const std::vector< int > &	indices,
		std::string const &	pdb_field,
		double const	pdb_field_value
	)

override

Definition at line 924 of file colvarproxy_namd.C.

References PDB::atom(), e_pdb_beta, e_pdb_occ, e_pdb_x, e_pdb_y, e_pdb_z, PDB::num_atoms(), and pdb_field_str2enum().

 {
   if (pdb_field_str.size() == 0 && indices.size() == 0) {
     cvm::error("Bug alert: either PDB field should be defined or list of "
                "atom IDs should be available when loading atom coordinates!\n", COLVARS_BUG_ERROR);
   }
 
   e_pdb_field pdb_field_index;
   bool const use_pdb_field = (pdb_field_str.size() > 0);
   if (use_pdb_field) {
     pdb_field_index = pdb_field_str2enum(pdb_field_str);
   }
 
   // next index to be looked up in PDB file (if list is supplied)
   std::vector<int>::const_iterator current_index = indices.begin();
 
   PDB *pdb = new PDB(pdb_filename);
   size_t const pdb_natoms = pdb->num_atoms();
 
   if (pos.size() != pdb_natoms) {
 
     bool const pos_allocated = (pos.size() > 0);
 
     size_t ipos = 0, ipdb = 0;
     for ( ; ipdb < pdb_natoms; ipdb++) {
 
       if (use_pdb_field) {
         // PDB field mode: skip atoms with wrong value in PDB field
         double atom_pdb_field_value = 0.0;
 
         switch (pdb_field_index) {
         case e_pdb_occ:
           atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
           break;
         case e_pdb_beta:
           atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
           break;
         case e_pdb_x:
           atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
           break;
         case e_pdb_y:
           atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
           break;
         case e_pdb_z:
           atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
           break;
         default:
           break;
         }
 
         if ( (pdb_field_value) &&
              (atom_pdb_field_value != pdb_field_value) ) {
           continue;
         } else if (atom_pdb_field_value == 0.0) {
           continue;
         }
 
       } else {
         // Atom ID mode: use predefined atom IDs from the atom group
         if (((int) ipdb) != *current_index) {
           // Skip atoms not in the list
           continue;
         } else {
           current_index++;
         }
       }
 
       if (!pos_allocated) {
         pos.push_back(cvm::atom_pos(0.0, 0.0, 0.0));
       } else if (ipos >= pos.size()) {
         cvm::error("Error: the PDB file \""+
                    std::string(pdb_filename)+
                    "\" contains coordinates for "
                    "more atoms than needed.\n", COLVARS_BUG_ERROR);
       }
 
       pos[ipos] = cvm::atom_pos((pdb->atom(ipdb))->xcoor(),
                                 (pdb->atom(ipdb))->ycoor(),
                                 (pdb->atom(ipdb))->zcoor());
       ipos++;
       if (!use_pdb_field && current_index == indices.end())
         break;
     }
 
     if (ipos < pos.size() || (!use_pdb_field && current_index != indices.end())) {
       size_t n_requested = use_pdb_field ? pos.size() : indices.size();
       cvm::error("Error: number of matching records in the PDB file \""+
                  std::string(pdb_filename)+"\" ("+cvm::to_str(ipos)+
                  ") does not match the number of requested coordinates ("+
                  cvm::to_str(n_requested)+").\n", COLVARS_INPUT_ERROR);
       return COLVARS_ERROR;
     }
   } else {
 
     // when the PDB contains exactly the number of atoms of the array,
     // ignore the fields and just read coordinates
     for (size_t ia = 0; ia < pos.size(); ia++) {
       pos[ia] = cvm::atom_pos((pdb->atom(ia))->xcoor(),
                               (pdb->atom(ia))->ycoor(),
                               (pdb->atom(ia))->zcoor());
     }
   }
 
   delete pdb;
   return COLVARS_OK;
 }

◆ log()

void colvarproxy_namd::log ( std::string const & message )

override

Definition at line 693 of file colvarproxy_namd.C.

References endi(), and iout.

Referenced by calculate(), error(), setup(), and update_atom_properties().

 {
   std::istringstream is(message);
   std::string line;
   while (std::getline(is, line))
     iout << "colvars: " << line << "\n";
   iout << endi;
 }

◆ num_replicas()

int colvarproxy_namd::num_replicas ( )

override

Definition at line 1628 of file colvarproxy_namd.C.

                                    {
   return CmiNumPartitions();
 }

◆ output_stream()

std::ostream & colvarproxy_namd::output_stream	(	std::string const &	output_name,
		std::string const	description
	)

override

Definition at line 1093 of file colvarproxy_namd.C.

References backup_file(), and debug.

 {
   if (cvm::debug()) {
     cvm::log("Using colvarproxy_namd::output_stream()\n");
   }
 
   if (!io_available()) {
     cvm::error("Error: trying to access an output file/channel "
                "from the wrong thread.\n", COLVARS_BUG_ERROR);
     return *output_stream_error_;
   }
 
   if (output_streams_.count(output_name) > 0) {
     return *(output_streams_[output_name]);
   }
 
   backup_file(output_name.c_str());
 
   output_streams_[output_name] = new ofstream_namd(output_name.c_str(), std::ios::binary);
   if (! output_streams_[output_name]->good()) {
     cvm::error("Error: cannot write to "+description+" \""+output_name+"\".\n",
                COLVARS_FILE_ERROR);
   }
 
   return *(output_streams_[output_name]);
 }

◆ position_distance()

cvm::rvector colvarproxy_namd::position_distance	(	cvm::atom_pos const &	pos1,
		cvm::atom_pos const &	pos2
	)		const

Definition at line 862 of file colvarproxy_namd.C.

References Lattice::delta(), GlobalMaster::lattice, Vector::x, Vector::y, and Vector::z.

 {
   Position const p1(pos1.x, pos1.y, pos1.z);
   Position const p2(pos2.x, pos2.y, pos2.z);
   // return p2 - p1
   Vector const d = this->lattice->delta(p2, p1);
   return cvm::rvector(d.x, d.y, d.z);
 }

◆ rand_gaussian()

cvm::real colvarproxy_namd::rand_gaussian ( )

inlineoverride

Definition at line 115 of file colvarproxy_namd.h.

References Random::gaussian(), and random.

   {
     return random.gaussian();
   }

◆ replica_comm_barrier()

void colvarproxy_namd::replica_comm_barrier ( )

override

Definition at line 1633 of file colvarproxy_namd.C.

References replica_barrier().

                                             {
   replica_barrier();
 }

◆ replica_comm_recv()

int colvarproxy_namd::replica_comm_recv	(	char *	msg_data,
		int	buf_len,
		int	src_rep
	)

override

Definition at line 1638 of file colvarproxy_namd.C.

References DataMessage::data, replica_recv(), and DataMessage::size.

                                                      {
   DataMessage *recvMsg = NULL;
   replica_recv(&recvMsg, src_rep, CkMyPe());
   CmiAssert(recvMsg != NULL);
   int retval = recvMsg->size;
   if (buf_len >= retval) {
     memcpy(msg_data,recvMsg->data,retval);
   } else {
     retval = 0;
   }
   CmiFree(recvMsg);
   return retval;
 }

◆ replica_comm_send()

int colvarproxy_namd::replica_comm_send	(	char *	msg_data,
		int	msg_len,
		int	dest_rep
	)

override

Definition at line 1654 of file colvarproxy_namd.C.

References replica_send().

                                                       {
   replica_send(msg_data, msg_len, dest_rep, CkMyPe());
   return msg_len;
 }

◆ replica_index()

int colvarproxy_namd::replica_index ( )

override

Definition at line 1623 of file colvarproxy_namd.C.

                                     {
   return CmiMyPartition();
 }

◆ request_alch_energy_freq()

int colvarproxy_namd::request_alch_energy_freq ( int const freq )

Request energy computation every freq steps.

Request alchemical energy computation every freq steps.

Definition at line 1662 of file colvarproxy_namd.C.

References SimParameters::alchOn, SimParameters::alchThermIntOn, SimParameters::computeEnergies, and simparams.

                                                              {
   // This test is only valid for NAMD3
   if (freq % simparams->computeEnergies) {
     cvm::error("computeEnergies must be a divisor of lambda-dynamics period (" + cvm::to_str(freq) + ").\n");
     return COLVARS_INPUT_ERROR;
   }
   if (!simparams->alchOn) {
     cvm::error("alchOn must be enabled for lambda-dynamics.\n");
     return COLVARS_INPUT_ERROR;
   }
   if (!simparams->alchThermIntOn) {
     cvm::error("alchType must be set to TI for lambda-dynamics.\n");
     return COLVARS_INPUT_ERROR;
   }
   return COLVARS_OK;
 }

◆ request_total_force()

void colvarproxy_namd::request_total_force ( bool yesno )

override

Definition at line 680 of file colvarproxy_namd.C.

References debug, and GlobalMaster::requestTotalForce().

 {
   if (cvm::debug()) {
     cvm::log("colvarproxy_namd::request_total_force()\n");
   }
   total_force_requested = yesno;
   requestTotalForce(total_force_requested);
   if (cvm::debug()) {
     cvm::log("colvarproxy_namd::request_total_force() end\n");
   }
 }

◆ reset()

int colvarproxy_namd::reset ( )

override

Definition at line 313 of file colvarproxy_namd.C.

References atoms_map, ResizeArray< Elem >::clear(), debug, GlobalMaster::modifyAppliedForces(), GlobalMaster::modifyForcedAtoms(), GlobalMaster::modifyGridObjForces(), GlobalMaster::modifyGroupForces(), GlobalMaster::modifyRequestedAtoms(), GlobalMaster::modifyRequestedGridObjects(), GlobalMaster::modifyRequestedGroups(), and GlobalMaster::requestTotalForce().

 {
   if (cvm::debug()) {
     cvm::log("colvarproxy_namd::reset()\n");
   }
 
   int error_code = COLVARS_OK;
 
   // Unrequest all positions, total forces, etc from NAMD
   modifyRequestedAtoms().clear();
   modifyForcedAtoms().clear();
   modifyAppliedForces().clear();
 
   modifyRequestedGroups().clear();
   modifyGroupForces().clear();
 
 #if NAMD_VERSION_NUMBER >= 34471681
   modifyRequestedGridObjects().clear();
   modifyGridObjForces().clear();
 #endif
 
   requestTotalForce(false);
 
   atoms_map.clear();
 
   // Clear internal atomic data
   error_code |= colvarproxy::reset();
 
   return error_code;
 }

◆ run_colvar_callback()

int colvarproxy_namd::run_colvar_callback	(	std::string const &	name,
		std::vector< const colvarvalue *> const &	cvcs,
		colvarvalue &	value
	)

override

Definition at line 645 of file colvarproxy_namd.C.

 {
   return colvarproxy::tcl_run_colvar_callback(name, cvc_values, value);
 }

◆ run_colvar_gradient_callback()

int colvarproxy_namd::run_colvar_gradient_callback	(	std::string const &	name,
		std::vector< const colvarvalue *> const &	cvcs,
		std::vector< cvm::matrix2d< cvm::real > > &	gradient
	)

override

Definition at line 653 of file colvarproxy_namd.C.

 {
   return colvarproxy::tcl_run_colvar_gradient_callback(name, cvc_values,
                                                        gradient);
 }

◆ run_force_callback()

int colvarproxy_namd::run_force_callback ( )

override

Definition at line 640 of file colvarproxy_namd.C.

 {
   return colvarproxy::tcl_run_force_callback();
 }

◆ scalable_group_coms()

int colvarproxy_namd::scalable_group_coms ( )

inlineoverride

Definition at line 215 of file colvarproxy_namd.h.

   {
     return COLVARS_OK;
   }

◆ send_alch_lambda()

int colvarproxy_namd::send_alch_lambda ( void )

Set value of alchemical lambda parameter in back-end.

Definition at line 1688 of file colvarproxy_namd.C.

References SimParameters::alchLambda, SimParameters::alchLambdaFreq, and simparams.

                                            {
   if (simparams->alchLambdaFreq > 0) {
     cvm::error("Cannot set lambda from Colvars because alchLambdaFreq is enabled. "
                 "Either remove biasing forces and extended Lagrangian dynamics on the alchemical coordinate, "
                 "or disable alchLambdaFreq.\n");
     return COLVARS_INPUT_ERROR;
   } else {
     simparams->alchLambda = cached_alch_lambda;
   }
   return COLVARS_OK;
 }

◆ set_unit_system()

int colvarproxy_namd::set_unit_system	(	std::string const &	units_in,
		bool	check_only
	)

override

Definition at line 1305 of file colvarproxy_namd.C.

 {
   if (units_in != "real") {
     cvm::error("Error: Specified unit system \"" + units_in + "\" is unsupported in NAMD. Supported units are \"real\" (A, kcal/mol).\n");
     return COLVARS_ERROR;
   }
   return COLVARS_OK;
 }

◆ setup()

int colvarproxy_namd::setup ( )

override

Definition at line 234 of file colvarproxy_namd.C.

References SimParameters::dt, log(), GlobalMaster::modifyGridObjForces(), GlobalMaster::modifyRequestedGroups(), simparams, ResizeArray< Elem >::size(), update_atom_properties(), update_group_properties(), update_target_temperature(), and SimParameters::wrapAll.

Referenced by calculate(), and colvarproxy_namd().

 {
   int error_code = colvarproxy::setup();
 
   if (colvars->size() == 0) {
     // Module is empty, nothing to do
     return COLVARS_OK;
   }
 
   log("Updating NAMD interface:\n");
 
   errno = 0;
 
   if (simparams->wrapAll) {
     log("Warning: enabling wrapAll can lead to inconsistent results "
         "for Colvars calculations: please disable wrapAll, "
         "as is the default option in NAMD.\n");
   }
 
   log("updating atomic data ("+cvm::to_str(atoms_ids.size())+" atoms).\n");
 
   size_t i;
   for (i = 0; i < atoms_ids.size(); i++) {
     update_atom_properties(i);
 
     // zero out mutable arrays
     atoms_positions[i] = cvm::rvector(0.0, 0.0, 0.0);
     atoms_total_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
     atoms_new_colvar_forces[i] = cvm::rvector(0.0, 0.0, 0.0);
   }
 
   size_t n_group_atoms = 0;
   for (int ig = 0; ig < modifyRequestedGroups().size(); ig++) {
     n_group_atoms += modifyRequestedGroups()[ig].size();
   }
 
   log("updating group data ("+cvm::to_str(atom_groups_ids.size())+
       " scalable groups, "+
       cvm::to_str(n_group_atoms)+" atoms in total).\n");
 
   // Note: groupMassBegin, groupMassEnd may be used here, but they won't work for charges
   for (int ig = 0; ig < modifyRequestedGroups().size(); ig++) {
 
     // update mass and charge
     update_group_properties(ig);
 
     atom_groups_coms[ig] = cvm::rvector(0.0, 0.0, 0.0);
     atom_groups_total_forces[ig] = cvm::rvector(0.0, 0.0, 0.0);
     atom_groups_new_colvar_forces[ig] = cvm::rvector(0.0, 0.0, 0.0);
   }
 
 #if NAMD_VERSION_NUMBER >= 34471681
   log("updating grid object data ("+cvm::to_str(volmaps_ids.size())+
       " grid objects in total).\n");
   for (int imap = 0; imap < modifyGridObjForces().size(); imap++) {
     volmaps_new_colvar_forces[imap] = 0.0;
   }
 #endif
 
   size_t const new_features_hash =
     std::hash<std::string>{}(colvars->feature_report(0));
   if (new_features_hash != features_hash) {
     // Nag only once, there may be many run commands
     log(std::string("\n")+colvars->feature_report(0)+std::string("\n"));
     features_hash = new_features_hash;
   }
 
   update_target_temperature();
   log("updating target temperature (T = "+
       cvm::to_str(target_temperature())+" K).\n");
 
   // Note: not needed currently, but may be in the future if NAMD allows
   // redefining the timestep
   set_integration_timestep(simparams->dt);
 
   return error_code;
 }

◆ total_forces_enabled()

bool colvarproxy_namd::total_forces_enabled ( ) const

inlineoverride

Definition at line 102 of file colvarproxy_namd.h.

   {
     return total_force_requested;
   }

◆ update_accelMD_info()

void colvarproxy_namd::update_accelMD_info ( )

protected

Definition at line 622 of file colvarproxy_namd.C.

References Controller::accelMDdV, amd_weight_factor, and controller.

Referenced by calculate().

                                            {
   // This aMD factor is from previous step!
   amd_weight_factor = std::exp(controller->accelMDdV / (target_temperature() * boltzmann()));
 }

◆ update_atom_properties()

void colvarproxy_namd::update_atom_properties ( int index )

Definition at line 846 of file colvarproxy_namd.C.

References Molecule::atomcharge(), Molecule::atommass(), log(), Node::molecule, and Node::Object().

Referenced by init_atom(), setup(), and update_atoms_map().

 {
   Molecule *mol = Node::Object()->molecule;
   // update mass
   double const mass = mol->atommass(atoms_ids[index]);
   if (mass <= 0.001) {
     this->log("Warning: near-zero mass for atom "+
               cvm::to_str(atoms_ids[index]+1)+
               "; expect unstable dynamics if you apply forces to it.\n");
   }
   atoms_masses[index] = mass;
   // update charge
   atoms_charges[index] = mol->atomcharge(atoms_ids[index]);
 }

◆ update_atoms_map()

int colvarproxy_namd::update_atoms_map	(	AtomIDList::const_iterator	begin,
		AtomIDList::const_iterator	end
	)

Definition at line 198 of file colvarproxy_namd.C.

References ResizeArray< Elem >::add(), atoms_map, debug, init_atoms_map(), GlobalMaster::modifyRequestedAtoms(), Node::molecule, Molecule::numAtoms, Node::Object(), and update_atom_properties().

Referenced by calculate().

 {
   if (atoms_map.size() != Node::Object()->molecule->numAtoms) {
     init_atoms_map();
   }
 
   for (AtomIDList::const_iterator a_i = begin; a_i != end; a_i++) {
 
     if (atoms_map[*a_i] >= 0) continue;
 
     for (size_t i = 0; i < atoms_ids.size(); i++) {
       if (atoms_ids[i] == *a_i) {
         atoms_map[*a_i] = i;
         break;
       }
     }
 
     if (atoms_map[*a_i] < 0) {
       // this atom is probably managed by another GlobalMaster:
       // add it here anyway to avoid having to test for array boundaries at each step
       int const index = add_atom_slot(*a_i);
       atoms_map[*a_i] = index;
       modifyRequestedAtoms().add(*a_i);
       update_atom_properties(index);
     }
   }
 
   if (cvm::debug()) {
     cvm::log("atoms_map = "+cvm::to_str(atoms_map)+".\n");
   }
 
   return COLVARS_OK;
 }

◆ update_group_properties()

int colvarproxy_namd::update_group_properties ( int index )

Definition at line 1278 of file colvarproxy_namd.C.

References Molecule::atomcharge(), Molecule::atommass(), debug, GlobalMaster::modifyRequestedGroups(), Node::molecule, Node::Object(), and ResizeArray< Elem >::size().

Referenced by init_atom_group(), and setup().

 {
   AtomIDList const &namd_group = modifyRequestedGroups()[index];
   if (cvm::debug()) {
     cvm::log("Re-calculating total mass and charge for scalable group no. "+cvm::to_str(index+1)+" ("+
              cvm::to_str(namd_group.size())+" atoms).\n");
   }
 
   cvm::real total_mass = 0.0;
   cvm::real total_charge = 0.0;
   for (int i = 0; i < namd_group.size(); i++) {
     total_mass += Node::Object()->molecule->atommass(namd_group[i]);
     total_charge += Node::Object()->molecule->atomcharge(namd_group[i]);
   }
   atom_groups_masses[index] = total_mass;
   atom_groups_charges[index] = total_charge;
 
   if (cvm::debug()) {
     cvm::log("total mass = "+cvm::to_str(total_mass)+
              ", total charge = "+cvm::to_str(total_charge)+"\n");
   }
 
   return COLVARS_OK;
 }

◆ update_target_temperature()

int colvarproxy_namd::update_target_temperature ( )

Get the target temperature from the NAMD thermostats supported so far.

Definition at line 168 of file colvarproxy_namd.C.

References SimParameters::langevinOn, SimParameters::langevinTemp, SimParameters::loweAndersenOn, SimParameters::loweAndersenTemp, SimParameters::reassignFreq, SimParameters::reassignTemp, SimParameters::rescaleFreq, SimParameters::rescaleTemp, simparams, SimParameters::stochRescaleOn, SimParameters::stochRescaleTemp, SimParameters::tCoupleOn, and SimParameters::tCoupleTemp.

Referenced by colvarproxy_namd(), and setup().

 {
   int error_code = COLVARS_OK;
   if (simparams->rescaleFreq > 0) {
     error_code |= set_target_temperature(simparams->rescaleTemp);
   } else if (simparams->reassignFreq > 0) {
     error_code |= set_target_temperature(simparams->reassignTemp);
   } else if (simparams->langevinOn) {
     error_code |= set_target_temperature(simparams->langevinTemp);
   } else if (simparams->tCoupleOn) {
     error_code |= set_target_temperature(simparams->tCoupleTemp);
   } else if (simparams->loweAndersenOn) {
     error_code |= set_target_temperature(simparams->loweAndersenTemp);
   } else if (simparams->stochRescaleOn) {
     error_code |= set_target_temperature(simparams->stochRescaleTemp);
   } else {
     error_code |= set_target_temperature(0.0);
   }
   return error_code;
 }

Friends And Related Function Documentation

◆ cvm::atom

friend class cvm::atom

friend

Definition at line 76 of file colvarproxy_namd.h.

Referenced by load_atoms_pdb().

Member Data Documentation

◆ accelMDOn

bool colvarproxy_namd::accelMDOn

protected

Used to submit restraint energy as MISC.

Accelerated MD reweighting factor

Definition at line 68 of file colvarproxy_namd.h.

Referenced by accelMD_enabled(), calculate(), and colvarproxy_namd().

◆ amd_weight_factor

cvm::real colvarproxy_namd::amd_weight_factor

protected

Definition at line 69 of file colvarproxy_namd.h.

Referenced by colvarproxy_namd(), get_accelMD_factor(), and update_accelMD_info().

◆ atoms_map

std::vector<int> colvarproxy_namd::atoms_map

protected

Array of atom indices (relative to the colvarproxy arrays), usedfor faster copy of atomic data.

Definition at line 45 of file colvarproxy_namd.h.

Referenced by calculate(), init_atom(), init_atoms_map(), reset(), and update_atoms_map().

◆ controller

Controller const* colvarproxy_namd::controller

protected

Pointer to Controller object.

Definition at line 51 of file colvarproxy_namd.h.

Referenced by calculate(), get_dE_dlambda(), and update_accelMD_info().

◆ first_timestep

bool colvarproxy_namd::first_timestep

protected

Definition at line 56 of file colvarproxy_namd.h.

Referenced by calculate(), and colvarproxy_namd().

◆ previous_NAMD_step

cvm::step_number colvarproxy_namd::previous_NAMD_step

protected

Definition at line 57 of file colvarproxy_namd.h.

Referenced by calculate().

◆ random

Random colvarproxy_namd::random

protected

NAMD-style PRNG object.

Definition at line 54 of file colvarproxy_namd.h.

Referenced by colvarproxy_namd(), and rand_gaussian().

◆ simparams

SimParameters* colvarproxy_namd::simparams

protected

Pointer to the NAMD simulation input object.

Definition at line 48 of file colvarproxy_namd.h.

Referenced by add_energy(), calculate(), check_volmap_by_name(), colvarproxy_namd(), get_alch_lambda(), get_volmap_id_from_name(), init_volmap_by_name(), request_alch_energy_freq(), send_alch_lambda(), setup(), and update_target_temperature().

The documentation for this class was generated from the following files:

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ colvarproxy_namd()

◆ ~colvarproxy_namd()

Member Function Documentation

◆ accelMD_enabled()

◆ add_energy()

◆ backup_file()

◆ calculate()

◆ check_atom_id() [1/2]

◆ check_atom_id() [2/2]

◆ check_atom_name_selections_available()

◆ check_replicas_enabled()

◆ check_volmap_by_id()

◆ check_volmap_by_name()

◆ check_volmaps_available()

◆ clear_atom()

◆ clear_atom_group()

◆ clear_volmap()

◆ close_output_stream()

◆ close_output_streams()

◆ compute_volmap()

◆ error()

◆ flush_output_stream()

◆ flush_output_streams()

◆ get_accelMD_factor()

◆ get_alch_lambda()

◆ get_dE_dlambda()

◆ get_volmap_id_from_name()

◆ getGridForceGridValue()

◆ GridForceGridLoop()

◆ init_atom() [1/2]

◆ init_atom() [2/2]

◆ init_atom_group()

◆ init_atoms_map()

◆ init_tcl_pointers()

◆ init_volmap_by_id()

◆ init_volmap_by_name()

◆ load_atoms_pdb()

◆ load_coords_pdb()

◆ log()

◆ num_replicas()

◆ output_stream()

◆ position_distance()

◆ rand_gaussian()

◆ replica_comm_barrier()

◆ replica_comm_recv()

◆ replica_comm_send()

◆ replica_index()

◆ request_alch_energy_freq()

◆ request_total_force()

◆ reset()

◆ run_colvar_callback()

◆ run_colvar_gradient_callback()

◆ run_force_callback()

◆ scalable_group_coms()

◆ send_alch_lambda()

◆ set_unit_system()

◆ setup()

◆ total_forces_enabled()

◆ update_accelMD_info()

◆ update_atom_properties()

◆ update_atoms_map()

◆ update_group_properties()

◆ update_target_temperature()

Friends And Related Function Documentation

◆ cvm::atom

Member Data Documentation

◆ accelMDOn

◆ amd_weight_factor

◆ atoms_map

◆ controller

◆ first_timestep

◆ previous_NAMD_step

◆ random